Phylogenetics of small horseshoe bats from east Asia based on mitochondrial DNA sequence variation

We undertook analyses of mitochondrial DNA gene sequences and echolocation calls to resolve phylogenetic relationships among the related bat taxa Rhinolophus pusillus (sampled across China), R. monoceros (Taiwan), R. cornutus (main islands of Japan), and R. c. pumilus (Okinawa, Japan), Phylogenetic trees and genetic divergence analyses were constructed by combining new complete mitochondrial cytochrome-b gene sequences and partial mitochondrial control region sequences with published sequences. Our work showed that these 4 taxa formed monophyletic groups in the phylogenetic tree. However, low levels of sequence divergence among the taxa, together with similarities in body size and overlapping echolocation call frequencies, point to a lack of taxonomic distinctiveness. We therefore suggest that these taxa are better considered as geographical subspecies rather than distinct species, although this should not diminish the conservation importance of these island populations, which are important evolutionarily significant units. Based on our findings, we suggest that the similarities in body size and echolocation call frequency in these rhinolophids result from their recent common ancestry, whereas similarities in body size and call frequency with R. hipposideros of Europe are the result of convergent evolution.

An evaluation of the neocognitron

We describe a sequence of experiments investigating the strengths and limitations of Fukushima's neocognitron as a handwritten digit classifier. Using the results of these experiments as a foundation, we propose and evaluate improvements to Fukushima's original network in an effort to obtain higher recognition performance. The neocognitron's performance is shown to be strongly dependent on the choice of selectivity parameters and we present two methods to adjust these variables. Performance of the network under the more effective of the two new selectivity adjustment techniques suggests that the network fails to exploit the features that distinguish different classes of input data. To avoid this shortcoming, the network's final layer cells were replaced by a nonlinear classifier (a multilayer perceptron) to create a hybrid architecture. Tests of Fukushima's original system and the novel systems proposed in this paper suggest that it may be difficult for the neocognitron to achieve the performance of existing digit classifiers due to its reliance upon the supervisor's choice of selectivity parameters and training data. These findings pertain to Fukushima's implementation of the system and should not be seen as diminishing the practical significance of the concept of hierarchical feature extraction embodied in the neocognitron. © 1997 IEEE.

Characterization of frequency‐dependent magnetic susceptibility in UXO electromagnetic geophysics

Soils at many locations that have their origin in volcanic parent material and have undergone extensive weathering often exhibit strong frequency-dependent magnetic susceptibilities. The presence of such susceptibility has a profound effect on electromagnetic induction data acquired in such environments. Their transient electromagnetic response is characterized by a t-1 decay that is strong enough to mask UXO responses. In a field study and associated laboratory work on characterizing the frequency-dependent magnetic susceptibility and its influence on transient electromagnetic data, we collected soil samples on the surface and in soil pits from the Island of Kaho'olawe, Hawaii, and measured their frequency dependent magnetic susceptibilities. We present the details of the field investigation, confirm previous theoretical work with field and laboratory measurements, characterize the susceptibility with a Cole-Cole model, and investigate the response specific to the measured susceptibility.

Binding mechanism of affinity ligands for purification of plasmid DNA

Plasmid DNA for therapeutic and vaccination purposes must be highly purified. The high selectivity of affinity chromatography makes it ideal for the isolation of pDNA from complex biological feed stocks. Affinity chromatography makes use of the biological function and/or individual chemical structure of the interacting molecules. However, the success of any affinity purification protocol is dependent on the availability of suitable ligands. In this study, surface plasmon resonance (SPR) based Biacore system has been employed for the detection and quantification of the binding between lac operon (lacO) sequence contained in a pDNA and synthetic peptides based on the DNA-binding domain of the lac repressor protein, lad. The equilibrium dissociation constant (K D) and association and dissociation rate constants (ka, kd) for the interaction between plasmid DNA and designed peptides were determined.

Inferring phylogenies of evolving sequences without multiple sequence alignment

Alignment-free methods, in which shared properties of sub-sequences (e.g. identity or match length) are extracted and used to compute a distance matrix, have recently been explored for phylogenetic inference. However, the scalability and robustness of these methods to key evolutionary processes remain to be investigated. Here, using simulated sequence sets of various sizes in both nucleotides and amino acids, we systematically assess the accuracy of phylogenetic inference using an alignment-free approach, based on D2 statistics, under different evolutionary scenarios. We find that compared to a multiple sequence alignment approach, D2 methods are more robust against among-site rate heterogeneity, compositional biases, genetic rearrangements and insertions/deletions, but are more sensitive to recent sequence divergence and sequence truncation. Across diverse empirical datasets, the alignment-free methods perform well for sequences sharing low divergence, at greater computation speed. Our findings provide strong evidence for the scalability and the potential use of alignment-free methods in large-scale phylogenomics.

Learning the learning rate for prediction with expert advice

Most standard algorithms for prediction with expert advice depend on a parameter called the learning rate. This learning rate needs to be large enough to fit the data well, but small enough to prevent overfitting. For the exponential weights algorithm, a sequence of prior work has established theoretical guarantees for higher and higher data-dependent tunings of the learning rate, which allow for increasingly aggressive learning. But in practice such theoretical tunings often still perform worse (as measured by their regret) than ad hoc tuning with an even higher learning rate. To close the gap between theory and practice we introduce an approach to learn the learning rate. Up to a factor that is at most (poly)logarithmic in the number of experts and the inverse of the learning rate, our method performs as well as if we would know the empirically best learning rate from a large range that includes both conservative small values and values that are much higher than those for which formal guarantees were previously available. Our method employs a grid of learning rates, yet runs in linear time regardless of the size of the grid.

Experimental and numerical investigation of strain-rate dependent mechanical properties of single living cells

The objective of this project is to investigate the strain-rate dependent mechanical behaviour of single living cells using both experimental and numerical techniques. The results revealed that living cells behave as porohyperlastic materials and that both solid and fluid phases within the cells play important roles in their mechanical responses. The research reported in this thesis provides a better understanding of the mechanisms underlying the cellular responses to external mechanical loadings and of the process of mechanical signal transduction in living cells. It would help us to enhance knowledge of and insight into the role of mechanical forces in supporting tissue regeneration or degeneration.

Estimating link-dependent origin-destination matrices from sample trajectories and traffic counts

In transport networks, Origin-Destination matrices (ODM) are classically estimated from road traffic counts whereas recent technologies grant also access to sample car trajectories. One example is the deployment in cities of Bluetooth scanners that measure the trajectories of Bluetooth equipped cars. Exploiting such sample trajectory information, the classical ODM estimation problem is here extended into a link-dependent ODM (LODM) one. This much larger size estimation problem is formulated here in a variational form as an inverse problem. We develop a convex optimization resolution algorithm that incorporates network constraints. We study the result of the proposed algorithm on simulated network traffic.

Genome Sequence of Acinetobacter baumannii Strain A1, an Early Example of Antibiotic-Resistant Global Clone 1

Acinetobacter baumannii isolate A1 was recovered in the United Kingdom in 1982 and belongs to global clone 1 (GC1). Here, we present its complete 3.91-Mbp genome sequence, generated via a combination of short-read sequencing (Illumina), long-read sequencing (PacBio), and manual finishing.

Amygdala-dependent learning increases the number of spinophilin-immunoreactive dendritic spines in the lateral amygdala

During Pavlovian auditory fear conditioning a previously neutral auditory stimulus (CS) gains emotional significance through pairing with a noxious unconditioned stimulus (US). These associations are believed to be formed by way of plasticity at auditory input synapses on principal neurons in the lateral nucleus of the amygdala (LA). One proposed form of cellular plasticity involves structural changes in the number and morphology of dendritic spines...

GABAergic inhibition in the fear conditioning circuit of the lateral amygdala is potentiated by dopamine D1 agonists

Auditory fear conditioning is dependent on auditory signaling from the medial geniculate (MGm) and the auditory cortex (TE3) to principal neurons of the lateral amygdala (LA). Local circuit GABAergic interneurons are known to inhibit LA principal neurons via fast and slow IPSP's. Stimulation of MGm and TE3 produces excitatory post-synaptic potentials in both LA principal and interneurons, followed by inhibitory post-synaptic potentials. Manipulations of D1 receptors in the lateral and basal amygdala modulate the retrieval of learned association between an auditory CS and foot shock. Here we examined the effects of D1 agonists on GABAergic IPSP's evoked by stimulation of MGm and TE3 afferents in vitro. Whole cell patch recordings were made from principal neurons of the LA, at room temperature, in coronal brain slices using standard methods. Stimulating electrodes were placed on the fiber tracts medial to the LA and at the external capsule/layer VI border dorsal to the LA to activate (0.1-0.2mA) MGm and TE3 afferents respectively. Neurons were held at -55.0 mV by positive current injection to measure the amplitude of the fast IPSP. Changes in input resistance and membrane potential were measured in the absence of current injection. Stimulation of MGm or TE3 afferents produced EPSP's in the majority of principal neurons and in some an EPSP/IPSP sequence. Stimulation of MGm afferents produced IPSP's with amplitudes of -2.30 ± 0.53 mV and stimulation of TE3 afferents produced IPSP's with amplitudes of -1.98 ± 1.26 mV. Bath application of 20μM SKF38393 increased IPSP amplitudes to -5.94 ± 1.62 mV (MGm, n=3) and-5.46 ± 0.31 mV (TE3, n=3). Maximal effect occurred <10mins. A small increase in resting membrane potential and decrease in input resistance were observed. These data suggest that DA modulates both the auditory thalamic and auditory cortical inputs to the LA fear conditioning circuit via local GABAergic circuits. Supported by NIMH Grants 00956, 46516, and 58911.

How European public sector agencies innovate: The use of bottom-up, policy-dependent and knowledge-scanning innovation methods

Factor and cluster analysis are used to identify different methods that public sector agencies in Europeuse to innovate, based on data from a 2010 survey of 3273 agencies. The analyses identify three types ofinnovative agencies: bottom-up, knowledge-scanning, and policy-dependent. The distribution of bottom-up agencies across European countries is positively correlated with average per capita incomes while thedistribution of knowledge-scanning agencies is negatively correlated with income. In contrast, there isno consistent pattern by country in the distribution of policy-dependent agencies. Regression resultsthat control for agency characteristics find that innovation methods are significantly correlated with thebeneficial outcomes of innovation, with bottom-up and knowledge-scanning agencies out-performingpolicy-dependent agencies.

Anti-tumour effects of antibodies targeting the extracellular cysteine-rich region of the receptor tyrosine kinase EphB4

EphB4 is a membrane-bound receptor tyrosine kinase (RTK) commonly over-produced by many epithelial cancers but with low to no expression in most normal adult tissues. EphB4 over-production promotes ligand-independent signaling pathways that increase cancer cell viability and stimulate migration and invasion. Several studies have shown that normal ligand-dependent signaling is tumour suppressive and therefore novel therapeutics which block the tumour promoting ligand-independent signaling and/or stimulate tumour suppressive ligand-dependent signaling will find application in the treatment of cancer. An EphB4-specific polyclonal antibody, targeting a region of 200 amino acids in the extracellular portion of EphB4, showed potent in vitro anti-cancer effects measured by an increase in apoptosis and a decrease in anchorage independent growth. Peptide exclusion was used to identify the epitope targeted by this antibody within the cysteine-rich region of the EphB4 protein, a sequence defined as a potential ligand interacting interface. Addition of antibody to cancer cells resulted in phosphorylation and subsequent degradation of the EphB4 protein, suggesting a mechanism that is ligand mimetic and tumour suppressive. A monoclonal antibody which specifically targets this identified extracellular epitope of EphB4 significantly reduced breast cancer xenograft growth in vivo confirming that EphB4 is a useful target for ligand-mimicking antibody-based anti-cancer therapies.